QualFilter

Very simple quality filtering on paired reads when read1, read2, a single read, or both reads based on percentage of passed bases. Always keeps the paired reads together.

This is a modified C++ implementation of the read_qual_filter.py script for performance reasons.

Installation

First clone the repository:

git clone https://github.com/WEHIGenomicsRnD/qualfilter.git
cd qualfilter

Now you have to install the dependencies shargs and seqan3:

git clone --recurse-submodules https://github.com/seqan/sharg-parser.git
git clone --recurse-submodules https://github.com/seqan/seqan3.git

Now build the project:

./build.sh

This will build the binary file to build/qualfilter.

If you have permissions to install on your system you can also run:

cd build
make install

You can now run the test:

./test.sh

Usage

The test.sh shows example usage:

./build/qualfilter \
    -l test_data/sample_R1.fastq.gz \
    -r test_data/sample_R2.fastq.gz \
    -o test \
    -m both \
    -q 10 \
    -p 80

OPTIONS

  Input/output options:
    -l, --read1 (std::string)
          Read 1 FASTQ file.. The input file must exist and read permissions must be granted. Valid file extensions
          are: [fq.gz, fastq.gz, fq, fastq].
    -r, --read2 (std::string)
          Read 2 FASTQ file.. The input file must exist and read permissions must be granted. Valid file extensions
          are: [fq.gz, fastq.gz, fq, fastq].
    -o, --out-prefix (std::string)
          Prefix for output files.
    -m, --mode (std::string)
          Mode to run in. Default: "single". Value must be one of [read1, read2, single, both].
    -q, --min-qual (signed 32 bit integer)
          Quality score to filter on. Default: 30. Value must be in range [0,40].
    -p, --min-pass-percent (float)
          Minimum percent (0-100) of bases that must pass the quality filter. Default: 80. Value must be in range [0,100].

  Common options
    -h, --help
          Prints the help page.
    -hh, --advanced-help
          Prints the help page including advanced options.
    --version
          Prints the version information.
    --copyright
          Prints the copyright/license information.
    --export-help (std::string)
          Export the help page information. Value must be one of [html, man, ctd, cwl].
    --version-check (bool)
          Whether to check for the newest app version. Default: true